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3 Side Chain Conformation.

The side chain atoms of amino acids are named in the Greek alphabet according to this scheme.

Naming convention in protein side chains
Naming convention in side chains explained in a lysine-tyrosine strand. For clarity only heavy atoms are shown. Note that these two residues are from within a protein and thus have no terminal region.

The side chain torsion angles are named chi1, chi2,chi3, etc., as shown above. The chi1 angle is subject to certain restrictions which arise from steric hindrance between the gamma side chain atom(s) and the main chain. The different conformations of the side chain as a function of chi1 are referred to as gauche(+), trans and gauche(-). These are indicated in the diagrams below in which the amino acid is viewed along the Cbeta-Calpha bond.

Overview of different chi-angle conformations
Side chain conformations. Top left: Chi1-Chi2 plot for Lysine. The deepness of the blue indicates the frequency of this conformation found in protein structures. Bottom left: Schematic view into the Cbeta atom (top)-Calpha atom (hidden below) bond. Here the chi1 angle can easily be seen as the angle between the Nitrogen and Cgamma atom. Right: Examples of the three main conformations.

The most abundant conformation is gauche(+) in which the gamma side chain atom is opposite to the residue main chain carbonyl group when viewed along the Cbeta-Calpha bond.

The second most abundant conformation is trans in which the side chain gamma atom is opposite the main chain nitrogen.

The least abundant conformation is gauche(-) which occurs when the side chain is opposite the hydrogen substituent on the Calpha atom. This conformation is unstable because the gamma atom is in close contact with the main chain CO and NH groups. The gauche(-) conformation is occasionally adopted by serine or threonine residues in a helix where the steric hindrance is offset by a hydrogen bond between the gamma oxygen atom and the main chain.

With most amino acids the gauche(+) and trans conformations are adopted with similar abundances although the gauche(+) conformation tends to dominate.

Aliphatic amino acids which are bifurcated at Cbeta, i.e. valine and isoleucine, do not adopt the trans conformation very often as this involves one of the Cgamma atoms being in the unfavourable gauche(-) 'position'.

In general, side chains tend to adopt the same three torsion angles (+/-60 and 180 degrees) about chi2 since these correspond to staggered conformations. However, for residues with an sp2 hybridised gamma atom such as phenylalanine, tyrosine, etc., chi2 rarely equals 180 degrees because this would involve an eclipsed conformation. For these side chains the chi2 angle is usually close to +/-90 degrees as this minimises close contacts. For residues such as aspartate and asparagine the chi2 angles are strongly influenced by the hydrogen bonding capacity of the side chain and its environment. Consequently, these residues adopt a wide range of chi2 angles.